The nationwide Magic High Schools Thesis Competition held by the Japan Magic Association. Also known as just The Thesis Competition will be held in Kyoto. After experiencing the Thesis Competition being attacked by the Great Asian Alliance last year, Mikihiko, the head of the Disciplinary Committee, proposes to the Student Council that this year they would like to inspect the area around the venue in advance to ensure security. Tatsuya, Miyuki, Minami, Leo and Erika will also be accompanying him. On his way home after the Student Council meeting, Tatsuya learns from the news that Mayumi's bodyguard, Saburo Nakura, was murdered by someone in Kyoto.

As Tatsuya is researching the Traditionalist bases in Kyoto under Minoru's guidance, he meets the owner of a restaurant, who is also a Traditionalist, on the way to Kiyomizu Temple. The shop owner shares that he is concerned about the current state of Nara's Traditionalist sects being absorbed by casters from the Continent and offers to share information with Tatsuya. Based on the restaurant owner's information, Tatsuya narrows down a place in Kyoto where the Traditionalists are hiding. He meets with Mayumi, who wants to find the culprit who killed Nakura, and Masaki, who happened to come across them during a battle against the Traditionalists, and heads to Arashiyama with them.

The night before the Thesis Competition. Tatsuya receives a report from Fumiya that they have located Gongjin Zhou's whereabouts. He was hiding at the JGDF's 2nd Supply Base in Uji. Tatsuya speculates that he would not have enough offensive power to fight alone at the JGDF's base, so he contacts Masaki. When Masaki hears that they would need to invade an army base to get to him, he hesitates for a moment but decides to accompany Tatsuya to fulfill his responsibilities as a member of the Ten Master Clans. The two invade the army base where soldiers controlled by Gongji Zhou await...

Information gets out that Kanda, an anti-magic advocate and Diet member, will visit First High School with the media to observe the school's curriculum, claiming that he has heard disturbing rumors about it. He plans to create an uproar with the media and assert that the school is brainwashing students into the military - if he finds anything suspicious of that nature. To stop this ploy, Tatsuya suggests performing an experiment showing the students creating a Sustained Gravity Control-Type Magic Thermonuclear Fusion Reactor = Stellar Furnace. The students plan on demonstrating that the magic education they receive at the school can solve energy problems, and that magic can contribute to the peace of humankind depending on the type of magic they use.

A brother and a sister enroll at the Magic High School. In this school, the students are divided into two distinct groups as "Weeds" and "Blooms." Tatsuya, the brother, has a secret…

Mibu meets with Tatsuya at a cafe. She thanks him for defusing the brawl between her and Kirihara peacefully. She asks Tatsuya to join their kendo team. He suspects that she has an ulterior motive…

Nine Schools Competition has finally started, and all eyes are on First High School. Tatsuya learns that the intruders from previous night are with the No-Head Dragons. Will the competition continue without any more interruption?

During Women's Battle Board, Mari Watanabe has an accident and is taken to the Susono Base Hospital. Tatsuya helps her recover with magic. Still, she has to withdraw from Mirage Bat. Tatsuya suspects that the accident wasn't just an accident at all!

During the preparations for the Thesis Competition, a girl is seen carrying a wireless password breaker. Erika offers to teach Leo a move that would be lethal against his enemies. Since they are taking the day off together, rumors start flying about them!

Mibu tells Tatsuya that they are planning to let the school know of their thoughts about the discrimination among the students. An open forum is held at the school regarding the treatment of Course 1 and Course 2 students. However, there is an intrusion…

Tatsuya and the others go after the intruders. They are informed that the intruders are in the library, and Mibu is with them. Will they be able to stop them and find out what is going on?

Tatsuya has a plan to go after the people from Blance and take them on in battle. He leads the team to an abandoned factory where the people from Blance are. Will they be able to defeat them?

Nine Magic University Affiliated High Schools around the country are preparing for the upcoming Nine Schools Competition. The Student Council needs to select engineers. Since Tatsuya knows how to fine-tune CADs, will he take on the role of an engineer?

Tatsuya and Miyuki visit FLT where a Flying Spell experiment is taking place. They run into members of the Yotsuba family there. Tatsuya sees Mikihiko practicing Spirit Magic. Since Tatsuya seems to be interested, Mikihiko tells him about Crystal Eyes.

The bus that is carrying the students to the Nine Schools Competition is attacked by unknown forces. Tatsuya suspects that it is the work of an insider. At the banquet before the competition, students meet Kudou, the chairman of the Magic Association.

Thanks to Tatsuya's engineering skills, First High School players finish on the podium. Third High School students know that the success of First High is due to Tatsuya's skills. What will they do to beat First High School?

Tatsuya meets Masaki Ichijo and Shinkuro Kichijoji. It takes them by surprise that Tatsuya already knows about their background. Another accident happens at the Nine Schools Competition. First High students think that it was another act of sabotage.

Tatsuya is asked to compete in Monolith Code. He picks Leonhard and Mikihiko to be his team members. Kichijoji advises Ichijo to figure out a way to force Tatsuya into head-to-head combat to win Monolith Code. Will Tatsuya take the bait as expected?

Finally, the day has arrived for Monolith Code. Tatsuya and his teammates have a strategy against Cardinal George and the Crimson Prince. Miyuki is confident that her brother will be the winner. However, is there a bad surprise in store for First High?

Tatsuya has a feeling that an incident might occur during Mirage Bat. He assures Miyuki that he’ll protect her no matter what. Meanwhile, the No-Head Dragons decide to take even harsher actions to make sure that the Nine Schools Competition is called off.

First High School students celebrate their victories in the Nine Schools Competition. Enraged by the actions of No-Head Dragon, Tatsuya pays them a visit. Since Tatsuya is not a member of the Ten Master Clans, Jumonji has a very interesting offer for him.

Tatsuya's computer is hacked. He starts investigating the identity of the attackers and suspects that it has to do with the upcoming Thesis Competition. First High students sense that they are being watched. Will they be able to find out what is going on?

Tatsuya has brought the Relic to FLT. The lab is hacked by the Great Asian Alliance. An insider attempts to go through the personal belongings of Tatsuya at the Robot Research Club. Will the Relic be safe?

The Thesis Competition is underway and everyone is worried about the security for the event.

The battle rages on after the attack on the Yokohama Convention Center. Students fight to make it safely to the shelter while forces duke it on the streets.